The study examined Financial Resource allocation modalities in Church-Founded Secondary Schools in Uganda; the case of Kampala, Namirembe and Mukono dioceses. Adopting a cross-sectional survey design that utilized both quantitative and qualitative approaches, the study used simple random, stratified random and purposive sampling technics to select the various samples. Data was collected using; self-administered questionnaire, interview schedule, focus-group discussion and researcher observation checklist. The generated data was analysed using frequency counts, percentage scores and Pearson product moment correlation. The study findings revealed that purposeful financial resource allocation modalities through focused financial decision-making by relevant school stakeholders are fundamental in ensuring educational quality in church-founded secondary schools. It not only fosters equitable distribution of financial resources but also nurtures a smooth implementation of school programs, and leads to attainment of institutional set goals and educational effectiveness. The study thus recommended that church founded secondary schools ought to innovatively allocate financial and other resources to enhance their effectiveness.